Ultraconserved elements: analyses of dosage sensitivity, motifs and boundaries.
Ultraconserved elements (UCEs) are sequences that are identical between reference genomes of distantly related species. As they are under negative selection and enriched near or in specific classes of genes, one explanation for their ultraconservation may be their involvement in important functions. Indeed, many UCEs can drive tissue-specific gene expression. We have demonstrated that nonexonic UCEs are depleted among segmental duplications (SDs) and copy number variants (CNVs) and proposed that their ultraconservation may reflect a mechanism of copy counting via comparison. Here, we report that nonexonic UCEs are also depleted among 10 of 11 recent genomewide data sets of human CNVs, including 3 obtained with strategies permitting greater precision in determining the extents of CNVs. We further present observations suggesting that nonexonic UCEs per se may contribute to this depletion and that their apparent dosage sensitivity was in effect when they became fixed in the last common ancestor of mammals, birds, and reptiles, consistent with dosage sensitivity contributing to ultraconservation. Finally, in searching for the mechanism(s) underlying the function of nonexonic UCEs, we have found that they are enriched in TAATTA, which is also the recognition sequence for the homeodomain DNA-binding module, and bounded by a change in A + T frequency.
Chiang
Charleston W K
CW
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.
Derti
Adnan
A
Schwartz
Daniel
D
Chou
Michael F
MF
Hirschhorn
Joel N
JN
Wu
C-Ting
CT
D000818:Animals; D001483:Base Sequence; D002645:Chickens / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics*; D019143:Evolution, Molecular; D005091:Exons; D018628:Gene Dosage; D014644:Genetic Variation; D016678:Genome; D006801:Humans; D007438:Introns; D051379:Mice; D008969:Molecular Sequence Data; D051381:Rats; D017384:Sequence Deletion